I cannot 100% speak to NAPS, but you must have a nomination to be appointed to USMAPS. I am not sure the MOCs understand that as I see my MOC "Nominated" me to prep school and that is simply not true.
I am not sure how USNA views a MOC recommendation to NAPS. No Nom is needed for NAPS, it would simply a recommendation or endorsement. I would say best case scenario it might help a tiny bit and worst case it does nothing. The Admissions board will evaluate and make the recommendation for 3Q or not. If not they can recommend for prep. All you can do is wait and ensure that your DS said that prep would be a great option that he is willing to take.